1,275 research outputs found
A Tutorial on Bayesian Nonparametric Models
A key problem in statistical modeling is model selection, how to choose a
model at an appropriate level of complexity. This problem appears in many
settings, most prominently in choosing the number ofclusters in mixture models
or the number of factors in factor analysis. In this tutorial we describe
Bayesian nonparametric methods, a class of methods that side-steps this issue
by allowing the data to determine the complexity of the model. This tutorial is
a high-level introduction to Bayesian nonparametric methods and contains
several examples of their application.Comment: 28 pages, 8 figure
Search for patterns of functional specificity in the brain: A nonparametric hierarchical Bayesian model for group fMRI data
Functional MRI studies have uncovered a number of brain areas that demonstrate highly specific functional patterns. In the case of visual object recognition, small, focal regions have been characterized with selectivity for visual categories such as human faces. In this paper, we develop an algorithm that automatically learns patterns of functional specificity from fMRI data in a group of subjects. The method does not require spatial alignment of functional images from different subjects. The algorithm is based on a generative model that comprises two main layers. At the lower level, we express the functional brain response to each stimulus as a binary activation variable. At the next level, we define a prior over sets of activation variables in all subjects. We use a Hierarchical Dirichlet Process as the prior in order to learn the patterns of functional specificity shared across the group, which we call functional systems, and estimate the number of these systems. Inference based on our model enables automatic discovery and characterization of dominant and consistent functional systems. We apply the method to data from a visual fMRI study comprised of 69 distinct stimulus images. The discovered system activation profiles correspond to selectivity for a number of image categories such as faces, bodies, and scenes. Among systems found by our method, we identify new areas that are deactivated by face stimuli. In empirical comparisons with previously proposed exploratory methods, our results appear superior in capturing the structure in the space of visual categories of stimuli.McGovern Institute for Brain Research at MIT. Neurotechnology (MINT) ProgramNational Institutes of Health (U.S.) (Grant NIBIB NAMIC U54-EB005149)National Institutes of Health (U.S.) (Grant NCRR NAC P41-RR13218)National Eye Institute (Grant 13455)National Science Foundation (U.S.) (CAREER Grant 0642971)National Science Foundation (U.S.) (Grant IIS/CRCNS 0904625)Harvard University--MIT Division of Health Sciences and Technology (Catalyst Grant)American Society for Engineering Education. National Defense Science and Engineering Graduate Fellowshi
The Infinite Hierarchical Factor Regression Model
We propose a nonparametric Bayesian factor regression model that accounts for
uncertainty in the number of factors, and the relationship between factors. To
accomplish this, we propose a sparse variant of the Indian Buffet Process and
couple this with a hierarchical model over factors, based on Kingman's
coalescent. We apply this model to two problems (factor analysis and factor
regression) in gene-expression data analysis
Local Component Analysis
Kernel density estimation, a.k.a. Parzen windows, is a popular density
estimation method, which can be used for outlier detection or clustering. With
multivariate data, its performance is heavily reliant on the metric used within
the kernel. Most earlier work has focused on learning only the bandwidth of the
kernel (i.e., a scalar multiplicative factor). In this paper, we propose to
learn a full Euclidean metric through an expectation-minimization (EM)
procedure, which can be seen as an unsupervised counterpart to neighbourhood
component analysis (NCA). In order to avoid overfitting with a fully
nonparametric density estimator in high dimensions, we also consider a
semi-parametric Gaussian-Parzen density model, where some of the variables are
modelled through a jointly Gaussian density, while others are modelled through
Parzen windows. For these two models, EM leads to simple closed-form updates
based on matrix inversions and eigenvalue decompositions. We show empirically
that our method leads to density estimators with higher test-likelihoods than
natural competing methods, and that the metrics may be used within most
unsupervised learning techniques that rely on such metrics, such as spectral
clustering or manifold learning methods. Finally, we present a stochastic
approximation scheme which allows for the use of this method in a large-scale
setting
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